Ying He

Phd Student (Group member from 2007 until 2012) + 32 (0) 9 33 13 758 VIB / Ghent University Bioinformatics & Systems Biology Technologiepark 927 B-9052 Gent BELGIUM

CV

Birthday: 10th, June, 1982
Birth place: Shenyang, China
Education:

• Nov. 2007 - now: PhD in Bioinformatics and Evolutionary Genomics, University of Gent/VIB, Belgium
• Sep. 2005 - July 2007: MSc in Bioinformatics, Wageningen University, The Netherlands
  • July 2006 - Jan. 2007: Master thesis in Bioinformatics Group in WUR, supervisor Jack Leunissen
  • Jan.2007 - July 2007: Research project in Comparative Genomics Group in CMBI, supervisor Martijn Huynen
• Sep. 2001 - July 2005: BSc in Biotechnology, Dalian University of Technology, China

Research

General context

If all the genes in a genome are considered a dictionary for the language of life, then the syntactic and grammatical rules of that language would be equivalent to gene regulation. From a finite set of genes, many different phenotypes can emerge, depending on their spatiotemporal expression, the splicing of their transcripts, and the post-translational modifications of their protein products. Undoubtedly, Transcription Factors (TFs), as controllers of transcription initiation, influence such important biological functions as gene regulation and the complexity of development and differentiation. Therefore, it is no surprise that organismal complexity (in terms of number of distinct cell-types) correlates with an expansion of certain gene categories that are involved in gene regulation and signal transduction. Complexity also seems to correlate with the number and coverage of protein-protein interaction domains per protein. Various segments of a TF, like the DNA-binding domain, dimerization, activation, ligand-binding or other domains that are involved in protein-protein interactions are conserved at different levels.

Long term objectives

• Understand which parts of TFs underwent dramatic changes during key phases of plant macroevolution.
• Compare the trends that we observed in plants with trends observed in other eukaryotic lineages.

Short term objectives

• Study the evolution of phosphorylation sites using freely available phosphoproteomic experiments.
• Study the evolution of intrinsically disordered regions in TF families that are enriched in them.
• Study the evolution of protein-protein interaction domains in eukaryotic TF families.

Papers

(6) Cai, H., Liu, X., Vanneste, K., Proost, S., Tsai, C., Liu, K.-W., Chen, L.-J., He, Y., Xu, SX., Bian, C., Zheng, Z., Sun, F., Liu, W., , ., Pan, Z.-Y., Hsu, C.-C., Yang, Y.-P., Hsu, Y.-C., Chuang, Y.-C., Dievart, A., Dufayard, J.-F., Xu, SX., Wang, X., Wang, X., Xiao, X.-J., Zhao, X.-M., Du, Y., Zhang, G.-Q., Wang, X., Su, Y.-Y., Xie, G.-C., Liu, G.-H., Li, L.-Q., Huang, L.-Q., Luo, Y., Chen, H.-H., Van de Peer, Y., Liu, Z.-J. (2014) The genome sequence of the orchid Phalaenopsis equestris. Nat. Genet. 47(1):65–72.

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(5) Amoutzias, G., He, Y., Lilley, K., Van de Peer, Y., Oliver, S. (2012) Evaluation and properties of the budding yeast phosphoproteome. Molecular and Cellular Proteomics 11, M111.009555.

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(4) Bonnet, E., He, Y., Billiau, K., Van de Peer, Y. (2010) TAPIR, a web server for the prediction of plant microRNA targets, including target mimics. Bioinformatics 26(12):1566-8.

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(3) Amoutzias, G., He, Y., Gordon, J., Mossialos, D., Oliver, S., Van de Peer, Y. (2010) Posttranslational regulation impacts the fate of duplicated genes. Proc Natl Acad Sci 107(7):2967-71.

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(2) Kuzniar, A., Lin, K., He, Y., Nijveen, H., Pongor, S., Leunissen, J. (2009) ProGMap: an integrated annotation resource for protein orthology. Nucleic Acids Res. 37(Web Server issue):W428-34.

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(1) Dutilh, B., He, Y., Hekkelman, M., Huynen, M. (2008) Signature, a web server for taxonomic characterization of sequence samples using signature genes. Nucleic Acids Res. 36(Web Server issue):W470-4.

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